<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><base href="x-msg://548/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ben,<div><br></div><div>It is possible to load more than one assembly into one Ensembl database and we have a few examples, including:</div><div> human (homo_sapiens_core_73_37) - four assemblies </div><div> mouse (mus_musculus_core_73_38) - three assemblies</div><div> dog (canis_familiaris_core_73_31) - two assemblies</div><div> pig (sus_scrofa_core_73_102) - two assemblies</div><div> rat (rattus_norvegicus_core_73_5) - two assemblies</div><div><br></div><div>Are you looking to view two assemblies side-by-side as in our Region Comparison view? Here is pig vs human:</div><div> <a href="http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907">http://www.ensembl.org/Sus_scrofa/Share/3c8f1202250321838e0bc96d50392e89111929907</a></div><div><br></div><div>and here is a human assembly patch (HG79_PATCH) vs human primary assembly (chromosome 9):</div><div><a href="http://www.ensembl.org/Homo_sapiens/Share/ad39ce274b81b9a9247ee1095ec946ad111929907">http://www.ensembl.org/Homo_sapiens/Share/ad39ce274b81b9a9247ee1095ec946ad111929907</a></div><div><br></div><div><br></div><div>Below is some additional information on multiple assemblies in one database.</div><div><br></div><div>Let's take pig as an example. If you look here:</div><div><div> mysql -uanonymous -<a href="http://hensembldb.ensembl.org">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select * from coord_system"</div></div><div>you will see that we have two different coordinate system versions: Sscrofa9 and Sscrofa10.2. Each of these coordinate system versions represents a different assembly.</div><div><br></div><div><br></div><div>The coord_system table links to the seq_region table, which gives a list of all the sequences and components in each assembly. </div><div><div> mysql -uanonymous -<a href="http://hensembldb.ensembl.org">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select count(*),cs.name,cs.version from seq_region sr, coord_system cs where sr.coord_system_id=cs.coord_system_id group by cs.version,cs.name"</div><div>+----------+------------+-------------+</div><div>| count(*) | name | version |</div><div>+----------+------------+-------------+</div><div>| 186661 | contig | NULL |</div><div>| 21 | chromosome | Sscrofa10.2 |</div><div>| 9905 | scaffold | Sscrofa10.2 |</div><div>| 20 | chromosome | Sscrofa9 |</div><div>+----------+------------+-------------+</div></div><div>(We don't usually give the contigs a coord_system.version because they are often shared between multiple assemblies.)</div><div><br></div><div><br></div><div>It sounds like your assemblies have only one coord_system, scaffolds, whereas pig's Sscrofa9 has contigs and chromosomes and pig's Sscrofa10.2 assembly has contigs, scaffolds and chromosomes. The links between contigs, scaffolds and chromosomes are stored in the assembly table.</div><div><br></div><div><br></div><div><div>We also store which parts of the assemblies 'map' to one another. Within one assembly, the mapping between its contigs, scaffolds and chromosomes are provided in an "AGP" file given with the assembly. The chromosome-to-chromosome mapping (top line in the query below) was an additional step added by our Core team to link the two assemblies. We (Ensembl Core team) will be able to give you more information on how to do that.</div><div><div> mysql -uanonymous -<a href="http://hensembldb.ensembl.org">hensembldb.ensembl.org</a> -P3306 -Dsus_scrofa_core_73_102 -e "select meta_value from meta where meta_key = 'assembly.mapping'"</div><div>+---------------------------------------------+</div><div>| meta_value |</div><div>+---------------------------------------------+</div><div>| chromosome:Sscrofa10.2#chromosome:Sscrofa9 |</div><div>| chromosome:Sscrofa10.2#contig |</div><div>| chromosome:Sscrofa10.2|scaffold:Sscrofa10.2 |</div><div>| scaffold:Sscrofa10.2#contig |</div><div>+---------------------------------------------+</div></div></div><div><br></div><div>In order to load your two assemblies into one database, you'd need to set them with two different coord_system.version values. (Alternately, you could just load one assembly each into two databases.)</div><div><br></div><div>If the next step you're after is to view these two assemblies side-by-side, as in our Region Comparison view, additional information is required. Our Compara team usually align the two assemblies (LASTZ) and store the information in our 'compara' schema database. This information is used by the web code to generate the Region Comparison view. If you already know the scaffold-to-scaffold mapping for your two assemblies then I don't think you'd need to do the LASTZ alignment but I do think you'd need to still store the links in a compara-schema database. We (Ensembl Compara team) can help with that too.</div><div><br></div><div>Hope that helps as a start,</div><div>Bronwen (Genebuild team)</div><div><br></div><div><br></div><div><br><div><div>On 9 Sep 2013, at 02:18, Ben Warren <<a href="mailto:Ben.Warren@plantandfood.co.nz">Ben.Warren@plantandfood.co.nz</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-NZ" link="blue" vlink="purple" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi,<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I am running a local Ensembl instance using species data stored in a local database. Is it possible to add an additional ‘alternate’ assembly to an Ensembl species?<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">i.e.<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span><span>1.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span>I have created an assembly of scaffolds<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span><span>2.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span>I loaded that assembly into Ensembl as a new species<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span><span>3.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span>I have revised the assembly, altering the scaffolds<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: -18pt; "><span><span>4.<span style="font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-family: 'Times New Roman'; "> <span class="Apple-converted-space"> </span></span></span></span>I would like to view the alternate assembly ‘against’ the original assembly<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Is this possible? If so is there an example of this situation in an existing species on<span class="Apple-converted-space"> </span><a href="http://ensembl.org" style="color: purple; text-decoration: underline; ">ensembl.org</a>?<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Ben Warren</span></b><span style="font-size: 10pt; font-family: Arial, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Research Technologist<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; font-family: 'Times New Roman', serif; "> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span><img width="210" height="70" id="_x0000_i1025" src="file:///C:\Users\hrabxw\AppData\Roaming\Microsoft\Signatures\PFR-LOGO.gif" alt="Plant & Food Research"></span><span><o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">F: +64 9 925 7001<br><a href="mailto:ben.warren@plantandfood.co.nz" style="color: purple; text-decoration: underline; ">ben.warren@plantandfood.co.nz</a><br><a href="http://www.plantandfood.co.nz" style="color: purple; text-decoration: underline; ">www.plantandfood.co.nz</a><br>The New Zealand Institute for Plant & Food Research Limited<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; font-family: 'Times New Roman', serif; "> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">Postal Address:</span></b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; "><span class="Apple-converted-space"> </span>Plant & Food Research Mt Albert<br>Private Bag 92169, Auckland, 1142, New Zealand<br></span><b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">Physical Address:</span></b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; "><span class="Apple-converted-space"> </span>Plant & Food Research Mt Albert<br>120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><table><tbody><tr><td bgcolor="#ffffff"><font><pre>The contents of this e-mail are confidential and may be subject to legal privilege.
If you are not the intended recipient you must not use, disseminate, distribute or
reproduce all or any part of this e-mail or attachments. If you have received this
e-mail in error, please notify the sender and delete all material pertaining to this
e-mail. Any opinion or views expressed in this e-mail are those of the individual
sender and may not represent those of The New Zealand Institute for Plant and
Food Research Limited.</pre></font></td></tr></tbody></table>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" style="color: purple; text-decoration: underline; ">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev" style="color: purple; text-decoration: underline; ">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/" style="color: purple; text-decoration: underline; ">http://www.ensembl.info/</a><br></div></blockquote></div><br></div></body></html>